mwslawinska
commented
1 year ago Based on the html file, the issue is with the taxon ID that can't be inserted when submitting a job: "mysql error: [1048: Column 'taxon_ID' cannot be null] in EXECUTE("INSERT INTO jobs(data_ins,email,descr,taxon_ID,rules,world,type,inf_content,int_confidence,totalScore,status,location) VALUES (NOW(), NULL, NULL, NULL, NULL, NULL, 'batch', NULL, NULL, NULL, 'job scheduled', '0000')")". However, I have taxon: "3055" in the config file. Could you maybe give some suggestions how to deal with that?
Additional note: I tried submitting the generated file: blast/.tsv.zip and hmmer/hmm.out.zip files manually to Argot2.5 and I get warnings: "Truncating Blast input since the maximum number of sequences (10001) has been reached! Truncating HMMer input since the maximum number of sequences (10001) has been reached!". I suppose some of the genes will be missing then - is it an error in the GOMAP pipeline which can be fixed to avoid that?
GOMAP-singularity version: version 3.5.2.
GOMAP-singularity step questions is related to: mixmeth
The mixmeth step is completed and in argot2.5/ directory there are .tsv and .tsv.zip files in the blast /directory, .fa, .out, .out.zip in hmmer/ (generated in the mixmeth-preproc step) and .insert.html in html/, results/ is empty. However, I haven't gotten any e-mails from argot that the job was submitted/completed. @wkpalan, do you have any suggestions what could have gone wrong here?
The message I get about the submission: Running GOMAP --step=mixmeth --config=config.yml INFO: Convert SIF file to sandbox... Running mixed-method based annotations Submitting CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.1.tsv.zip and CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.1.hmm.out.zip to Argot2.5 INFO: Cleaning up image...